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In silico characterization of Wall-Associated kinases (WAKs) in Populus trichocarpa
Kévin Tocquard
To cite this version:
Kévin Tocquard. In silico characterization of Wall-Associated kinases (WAKs) in Populus trichocarpa.
17th Docotral school for life sciences, Health, Agronomy and Environment Days, Ecole Doctorale des Sciences de la Vie et de la Santé. FRA., May 2014, Clermont-Fd, France. 1 p. �hal-01268819�
Introduction
The wall-associated kinases (WAKs) are a set of receptor-like kinases (RLKs) involved in signaling pathways. WAKs have been described exhaustively in two herbaceous models, Arabidopsis thaliana and Oryza sativa (27 et 125 members, respectively). Various studies suggested that WAKs are able to bind pectins of the plant cell wall through a specific protein domain located in their extracellular region.
In woody species, WAKs, as receptors, may play a decisive part in development and in response to environmental constraints. The main characteristic of trees is wood production through secondary growth and perennialism, which implies short-term and long-lasting responses in continually changing environmental conditions. In addition, environmental stresses can induce specific modifications in secondary cell wall characteristics, notably G layer deposition in the tension wood, which requires cellular communications between the apoplasm and the cytoplasm. The involvement of WAKs as potential mediators of the reaction wood formation in response to gravitropic stimulus has been proposed.
In silico characterization of Wall-Associated Kinases (WAKs) in Populus trichocarpa
Tocquard Kévin Supervisors
Pr Roeckel-Drevet Patricia Dr Venisse Jean-Stéphane
He et al., 1999
cell wall cytoplasm signal peptide
EGF-like repeats
transmembrane domain kinase
Retrieval and sorting of PtWAK sequences
GubWAK WAK
EGFs T
M Kinase
WAKassoc
Protein domains
- GubWAK : adhesion site of WAKs to pectin - WAK : unknown function
- WAKassoc : unknown function
- EGFs : potentially involved in protein-protein interaction - TM : Transmembrane domain
- Kinase : phosphorylating domain
Extracellular
Intracellular
Group Specifications Gene number
PtWAK-RLK
(Receptor-like kinase) 119
PtWAK-RLCK
(Receptor-like cytoplasmic kinase) 32
PtWAK-RLP
(Receptor-like protein) 22
PtWAK short genes 2
Total number of WAKs 175
or or
0.1
Color ranges:
Poplar Rice
Arabidopsis
Potri.T112900.1
Potri.015G045100.1
Potri.015G044700.1 Potri.015G044800.1 Potri.T113200.1 Potri.T113100.1
Potri.012G054800.1 Potri.012G054700.1 Potri.010G120800.1
Potri.010G121100.1
Potri.017G118100.1 Potri.T064100.1
Potri.004G097100.1 Potri.004G096600.1
Potri.004G096900.1 Potri.017G118400.1
Potri.T064000.1 OsWAK1
OsW
AK10a
OsW
AK10b OsW
AK10c OsW
AK2 AtW
AKL21 AtW
AKL14
Potri.014G
038600.1
Potri.002G
130600.1
Potri.007G
034500.1
Potri.005G
130900.1 OsW
AK25
OsW AK
47 OsW
AK 59 OsW
AK 45 OsW
AK 49 OsW
AK 57
OsW
AK 42 OsW
AK 60 OsW
AK 46 OsW
AK 44
OsW
AK 43
OsW AK
51 OsW
AK 5 OsW
AK 8
OsW AK
64 OsW
AK 65
OsW AK
63 OsW
AK 12 OsW
AK 13
OsW AK
80
OsW
AK77 OsW
AK21 OsW
AK O 22
sWAK 24
OsWAK117 OsWAK116
OsWAK69
OsWAK123 OsWAK121
OsW
AK97 OsW
AK95 OsW
AK104
OsWAK 103 OsW
AK105 OsWAK
114
OsWAK99 OsWAK108 OsWAK
110
OsWAK126 OsWAK129a OsWAK26
OsWAK27
OsWAK61 OsWAK11
Potri.004G191500.1 Potri.004G191800.1
Potri.004G192400.1
Potri.004G192700.1 Potri.T167400.1
Potri.004G192900.1 Potri.004G191900.1 Potri.004G192100.1
Potri.004G193100.1 Potri.009G154100.1
Potri.009G154600.1
AtW AK L1 6
AtWAK3
AtW AK 1
AtW AK 5
AtW
AK
4
AtW AK
2
Po tri.002G
075900 .1 Po
tri.002G 076000
.1 AtWAKL22
AtWAKL2 AtWAKL4 AtWAKL5
AtWAKL1
AtWAKL3 AtWAKL10
AtWAKL9 AtWAKL13
AtWAKL17 AtWAKL18
AtWAKL11
AtWAKL8 Potri.009G154500.1 Potri.009G154300.1
Potri.009G157200.1
Potri.009G155000.1 Potri.003G186100.1 Potri.001G040800.1
Potri.T166600.1 Potri.001G040500.1
Potri.001G039200.1
Potri.001G038300.1 Potri.T132900.1
Potri.001G039900.1 Potri.T132800.1
Potri.T132700.1 Potri.001G041000.1 Potri.001G040900.1
Potri.001G040000.1 Potri.001G041100.1
Potri.T080500.1 Potri.00
3G185800.1
Potri.T080900.1 Potri.003G185700.1
Potri.004G192300.1 Potri.004G192500.1 Potri.T080700.1 Potri.T080600.1
Potri.003G186000.1
Potri.003G186200.1
Potri.T126500.1 Potri.018G148300.1
Potri.T126700.1
OsW AK29 OsW
AK28 OsW
AK6 OsW
AK9 OsW
AK56 OsW
AK14 OsW
AK15 OsW
AK16
OsW AK38 OsW
AK111 OsW
AK112b OsW
AK112d OsW
AK112a OsW
AK112c
OsW AK 75
OsW AK 87 OsW
AK73 OsW
AK76
OsW AK74 OsW
AK92 OsW
AK90 OsW
AK20 OsW
AK89a
OsW AK91 OsW
AK89b
OsW
AK55
OsWAK53a OsWAK53b Potri.006G118500.1
AtWAKL15
AtWAKL20
Potri.006G090200.1 Potri.008G059900.1
Potri.0
15G018
000.1 Potri.T
1364 00.1
Potri.0 12G
0034 00.1 Potri.0
12G 0035
00.1 Potri.012G
0028 00.1 Potri.012G
0030 00.1 Potri.T
1365 00.1 Potri.015G
0182 00.1 Potri.T
136600.1
Potri.017G
034700.1 Potri.017G
035500.1 Potri.007G
126200.1 Potri.007G
125100.1 Potri.007G
125600.1
Potri.0 12G
0546 00.1 Potri.T
1130 00.1 Potri.T
1128 00.1 Potri.0
15G 0452
00.1 Po
tri.017G 116900
.1 Po
tri.004G 097000
.1
Po tri.T
064900
.1 P otri.T
065000 .1
Po tri.017G
117500 .1
Po tri.T
064600 .1 Po
tri.017G 117300
.1 Po
tri.T 065200
.1 Po
tri.017G 117700
.1 Po
tri.T 064400
.1 Potri.0
10G 1209
00.1
Potri.0 10G
1210 00.1 Potri.0
04G 0764
00.1
Potri.0 04G
0765 00.1
Po tri.017G
034600
.1 P otri.017G
034500 .1
Po tri.017G
035400 .1
Po tri.0 07 G125500
.1 P otri. 00 7G 12 54 00 .1
Po tri.0 07 G125800
.1
Po tri.0 07 G1 25 20 0.1
Po tri.0 07 G1 25 00 0.1
Potri.015G018600.1 Potri.T136800.1
Potri.007G140900.1 Potri.007G140800.1
Potri.017G009600.1 Potri.017G009500.1
Potri.017G008000.1
Potri.017G009000.1
Potri.017G009200.1
Potri.017G008600.1 Potri.017G008200.1
Potri.017G007900.1
Potri.017G008400.1 Potri.017G008700.1
Potri.017G009400.1 Potri.017G009100.1
Po tri.0 07 G1 41 10 0.1 Po tri.0 07 G1 41 00 0.1
Potri.007G141500.1 Potri.007G141400.1 Po
tri.0 07 G1 17 00 0.1 Po tri.0 07 G1 17 10 0.1
Po tri.010G
118300 .1
Po tri.008G
125500 .1 Clade I
Clade II
Phylogenetic analyses
Phylogenetic tree of poplar WAKs
The protein domain architecture is indicated on the right of the phylogeny. Bar length and color shapes are proportional to the number of amino acids and the prediction of domain length, respectively. The tree obtained by the Bayesian inference method is represented.
Phylogenetic tree of poplar, rice and Arabidopsis WAKs
The tree obtained by the Bayesian inference method is represented.
Two monophyletic clades are markedly differentiated (i.e. WAK Clades I and II). A phylogenetic analysis of poplar, rice and Arabidopsis WAKs was also carried out.
WAK clade I contains members from the three species while WAK clade II contains only PtWAKs. This suggests that the evolution of sequences in the WAK clade I occurred in the monocot-dicot common ancestor, while the sequence in the WAK clade II evolved independently in poplar.
2.6 1.3 0.0
Potri.017G008700 Potri.015G045200 Potri.001G040500 Potri.T132900 Potri.017G034700 Potri.017G035500 Potri.009G154100 Potri.001G040000 Potri.017G118400
Potri.007G141100_Potri.007G141000 Potri.002G076000
Potri.017G035400 Potri.012G003000 Potri.017G117500
Potri.017G117200_Potri.017G117100 Potri.012G002800
Potri.012G003500 Potri.007G126200 Potri.004G191400 Potri.017G009200 Potri.014G038600 Potri.T064100 Potri.008G059900
Potri.007G140900_Potri.007G140800 Potri.004G191900
Potri.002G130600 Potri.004G191800 Potri.001G038300 Potri.005G130900 Potri.003G186100 Potri.005G203300 Potri.012G003700 Potri.004G192100 Potri.017G009400 Potri.T080500 Potri.015G018100 Potri.018G148300 Potri.007G125900 Potri.007G125100 Potri.007G125800 Potri.015G018600 Potri.017G009100
0.0 0.5 1.0
1.0 1.1 1.2
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Transcriptomics data analyses
WAK Clade I
WAK Clade II
Although the phylogenetic analysis is calculated on the kinase domain, some monophyletic groups preferentially contained one type of extracellular domain combination, suggesting a parallel evolution between the intracellular kinase domain and extracellular domains of PtWAK-RLK.
Conclusion
WAKs features described above make WAKs appealing candidates to investigate new communication networks that may relay the cell wall status to the cytoplasm. The cell wall is an essential compartment affected by many biotic constrains such as pathogen attacks or developmental processes but also by abiotic stresses such as drought and various mechanical stimulations.
Our study provides new insights into the WAK gene family in Populus. Our findings may be a starting point for a study of the physiological roles of WAKs in cellular regulatory networks in woody species.
References
Tocquard K, Lafon-Placette C, Auguin D, Muries B, Bronner G, Lopez D, Fumanal B, Franchel J, Bourgerie S, Maury S, Label P, Julien JL, Roeckel-Drevet P, Venisse JS (2014) In silico study of wall-associated kinase family reveals large- scale genomic expansion potentially connected with functional diversification in Populus. Tree Genetics &
Genomes. DOI: 10.1007/s11295-014-0748-7.
Tocquard K, Lopez D, Decourteix M, Thibaut B, Julien JL, Label P, Leblanc-Fournier N, Roeckel-Drevet P (2014) The molecular mechanism of reaction wood induction. The biology of reaction wood. Springer Berlin Heidelberg, p 107- 138
Clustered heatmap showing expression patterns of significant tissue/condition/genotype specific expressed in poplar
Only PtWAKs showing differential expression in at least one tissue/environmental condition/genotype are displayed (42 PtWAKs). Scale from 0.0 to 1.0 corresponds to drought experiment in the apex; scale from 1.0 to 1.2 is for all the Affymetrix array experiments. An asterisk indicates significant tissue/environmental condition/genotype effect on PtWAK expression according to Welch’s t-test/one-way ANOVA for two or more samples followed by adjusted Bonferroni correction (* p < 0.05). Hierarchical clustering was performed for PtWAKs according to their expression patterns.
‘Carpaccio’, ‘DN34’ and ‘Soligo’ are Populus canadensis genotypes, ‘NM36’ is P. nigra × P. maximowiczii while ‘AP-947’, ‘AP-1005’, ‘AP-1006’, ‘AP-2278’,
‘AP-2298’ and ‘AP-2300’ are P. balsamifera genotypes. Blue- and red-shaded PtWAK names belong to PtWAK-RLK and PtWAK-RLCK gene groups, respectively.
Twenty-five PtWAKs showed a differential expression in at least on tissue, mainly an over-expression in mature leaves, roots and flowers, 16 PtWAKs were significantly affected by changing environmental conditions, and 24 were modulated differentially between poplar genotypes.
Interestingly, PtWAK that showed a modulated expression after pathogen attack and PtWAK that are modulated during developmental/growth processes belong to WAK clade II (specific to poplar) and WAK clade I (shared with Arabidopsis and rice), respectively. This is in accordance with what have been shown for the global receptor-like kinase (RLK) family, suggesting that members of a gene family developed in a species-specific way correspond to species-specific needs.
Collaborations